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A robust adaptive fuzzy neural network (RAFNN) backstepping control system is proposed to control the position of an X-Y-Theta motion control stage using linear ultrasonic motors (LUSMs) to track various contours in this study. First, an X-Y-Theta motion control stage is introduced. Then, the single-axis dynamics of LUSM mechanism with the introduction of a lumped uncertainty, which includes cross-coupled interference and friction force, is derived. Moreover, a conventional backstepping approach is proposed to compensate the uncertainties occurred in the motion control system. Furthermore, to improve the control performance in the tracking of the reference contours, an RAFNN backstepping control system is proposed to remove the chattering phenomena caused by the sign function in the backstepping control law. In the proposed RAFNN backstepping control system, a Sugeno-type adaptive fuzzy neural network (SAFNN) is employed to estimate the lumped uncertainty directly and a compensator is utilized to confront the reconstructed error of the SAFNN. In addition, the motions at the X axis, Y axis, and Theta axis are controlled separately. The experimental results show that the contour tracking performance is significantly improved and the robustness to parameter variations, external disturbances, cross-coupled interference, and friction force can be obtained, as well using the proposed RAFNN backstepping control system.